pdb

Bindings for core::io::pdb namespace

class pyrosetta.rosetta.core.io.pdb.Field

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.io.pdb.Field, : pyrosetta.rosetta.core.io.pdb.Field) pyrosetta.rosetta.core.io.pdb.Field

C++: core::io::pdb::Field::operator=(const struct core::io::pdb::Field &) –> struct core::io::pdb::Field &

property end
set_value_from_pdb_line(self: pyrosetta.rosetta.core.io.pdb.Field, source: str) None

Read field value from given .pdb line and set.

C++: core::io::pdb::Field::set_value_from_pdb_line(std::string) –> void

property start
property value
class pyrosetta.rosetta.core.io.pdb.RecordCollection

Bases: pyrosetta.rosetta.utility.SingletonBase_core_io_pdb_RecordCollection_t

This class is a singleton and manages the definitions of PDB Records, which should only be read from the database one time.

static get_instance() core::io::pdb::RecordCollection

C++: utility::SingletonBase<core::io::pdb::RecordCollection>::get_instance() –> class core::io::pdb::RecordCollection *

static is_valid_record_type(type: str) bool

Is the given string a valid 6-letter PDB record type?

C++: core::io::pdb::RecordCollection::is_valid_record_type(const std::string &) –> bool

class pyrosetta.rosetta.core.io.pdb.RecordType

Bases: pybind11_builtins.pybind11_object

Enumerators for all of the record types used in PDB files, according to:

http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html

Members:

HEADER

OBSLTE

TITLE

SPLIT

CAVEAT

COMPND

SOURCE

KEYWDS

EXPDTA

NUMMD

MDLTYP

AUTHOR

REVDAT

SPRSDE

JRNL

REMARK

DBREF

DBREF1

DBREF2

SEQADV

SEQRES

MODRES

HET

HETNAM

HETSYN

FORMUL

HELIX

SHEET

SSBOND

LINK

CISPEP

SITE

CRYST1

ORIGX1

ORIGX2

ORIGX3

SCALE1

SCALE2

SCALE3

MTRIX1

MTRIX2

MTRIX3

MODEL

ATOM

ANISOU

TER

HETATM

ENDMDL

CONECT

MASTER

END

UNKNOW

N_RECORD_TYPES

ANISOU = <RecordType.ANISOU: 45>
ATOM = <RecordType.ATOM: 44>
AUTHOR = <RecordType.AUTHOR: 12>
CAVEAT = <RecordType.CAVEAT: 5>
CISPEP = <RecordType.CISPEP: 31>
COMPND = <RecordType.COMPND: 6>
CONECT = <RecordType.CONECT: 49>
CRYST1 = <RecordType.CRYST1: 33>
DBREF = <RecordType.DBREF: 17>
DBREF1 = <RecordType.DBREF1: 18>
DBREF2 = <RecordType.DBREF2: 19>
END = <RecordType.END: 51>
ENDMDL = <RecordType.ENDMDL: 48>
EXPDTA = <RecordType.EXPDTA: 9>
FORMUL = <RecordType.FORMUL: 26>
HEADER = <RecordType.HEADER: 1>
HELIX = <RecordType.HELIX: 27>
HET = <RecordType.HET: 23>
HETATM = <RecordType.HETATM: 47>
HETNAM = <RecordType.HETNAM: 24>
HETSYN = <RecordType.HETSYN: 25>
JRNL = <RecordType.JRNL: 15>
KEYWDS = <RecordType.KEYWDS: 8>
MASTER = <RecordType.MASTER: 50>
MDLTYP = <RecordType.MDLTYP: 11>
MODEL = <RecordType.MODEL: 43>
MODRES = <RecordType.MODRES: 22>
MTRIX1 = <RecordType.MTRIX1: 40>
MTRIX2 = <RecordType.MTRIX2: 41>
MTRIX3 = <RecordType.MTRIX3: 42>
NUMMD = <RecordType.NUMMD: 10>
N_RECORD_TYPES = <RecordType.UNKNOW: 52>
OBSLTE = <RecordType.OBSLTE: 2>
ORIGX1 = <RecordType.ORIGX1: 34>
ORIGX2 = <RecordType.ORIGX2: 35>
ORIGX3 = <RecordType.ORIGX3: 36>
REMARK = <RecordType.REMARK: 16>
REVDAT = <RecordType.REVDAT: 13>
SCALE1 = <RecordType.SCALE1: 37>
SCALE2 = <RecordType.SCALE2: 38>
SCALE3 = <RecordType.SCALE3: 39>
SEQADV = <RecordType.SEQADV: 20>
SEQRES = <RecordType.SEQRES: 21>
SHEET = <RecordType.SHEET: 28>
SITE = <RecordType.SITE: 32>
SOURCE = <RecordType.SOURCE: 7>
SPLIT = <RecordType.SPLIT: 4>
SPRSDE = <RecordType.SPRSDE: 14>
SSBOND = <RecordType.SSBOND: 29>
TER = <RecordType.TER: 46>
TITLE = <RecordType.TITLE: 3>
UNKNOW = <RecordType.UNKNOW: 52>
property name
pyrosetta.rosetta.core.io.pdb.add_to_multimodel_pdb(*args, **kwargs)

Overloaded function.

  1. add_to_multimodel_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str, model_tag: str) -> bool

  2. add_to_multimodel_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str, model_tag: str, clear_existing_structures: bool) -> bool

Adds a pose to a multimodel pdb file (or creates the file)

Use default StructFileRepOptions

C++: core::io::pdb::add_to_multimodel_pdb(const class core::pose::Pose &, const std::string &, const std::string &, bool) –> bool

  1. add_to_multimodel_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str, model_tag: str, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> bool

  2. add_to_multimodel_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str, model_tag: str, options: pyrosetta.rosetta.core.io.StructFileRepOptions, clear_existing_structures: bool) -> bool

Adds a pose to a multimodel pdb file (or creates the file)

C++: core::io::pdb::add_to_multimodel_pdb(const class core::pose::Pose &, const std::string &, const std::string &, class std::shared_ptr<const class core::io::StructFileRepOptions>, bool) –> bool

  1. add_to_multimodel_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, model_tag: str) -> None

Adds a pose to a multimodel pdb file

Use default StructFileRepOptions

C++: core::io::pdb::add_to_multimodel_pdb(const class core::pose::Pose &, std::ostream &, const std::string &) –> void

  1. add_to_multimodel_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, model_tag: str, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

Adds a pose to a multimodel pdb file

C++: core::io::pdb::add_to_multimodel_pdb(const class core::pose::Pose &, std::ostream &, const std::string &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

pyrosetta.rosetta.core.io.pdb.build_pose_from_pdb_as_is(*args, **kwargs)

Overloaded function.

  1. build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, filename: str) -> None

Builds a pose into <pose>, without repacking or optimizing

hydrogens; using the full-atom ResidueTypeSet

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const std::string &) –> void

  1. build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, filename: str, pdr_options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> None

Builds a pose into <pose>, without repacking or optimizing

hydrogens; using the full-atom ResidueTypeSet and a set of options.

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const std::string &, const class core::io::StructFileReaderOptions &) –> void

  1. build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str) -> None

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const std::string &) –> void

  1. build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, pdr_options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> None

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const std::string &, const class core::io::StructFileReaderOptions &) –> void

  1. build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, file_contents: pyrosetta.rosetta.std.istream, pdr_options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> None

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const std::string &, std::istream &, const class core::io::StructFileReaderOptions &) –> void

pyrosetta.rosetta.core.io.pdb.create_pdb_contents_from_sfr(*args, **kwargs)

Overloaded function.

  1. create_pdb_contents_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep) -> str

  2. create_pdb_contents_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> str

Create a full .pdb as a string given a StructFileRep object.

C++: core::io::pdb::create_pdb_contents_from_sfr(const class core::io::StructFileRep &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> std::string

pyrosetta.rosetta.core.io.pdb.create_sfr_from_pdb_file_contents(*args, **kwargs)

Overloaded function.

  1. create_sfr_from_pdb_file_contents(pdb_contents: str, options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> pyrosetta.rosetta.core.io.StructFileRep

Create a representation of structural file data from .pdb file contents with options.

C++: core::io::pdb::create_sfr_from_pdb_file_contents(const std::string &, const class core::io::StructFileReaderOptions &) –> class core::io::StructFileRep

  1. create_sfr_from_pdb_file_contents(pdb_contents: str) -> pyrosetta.rosetta.core.io.StructFileRep

Create a representation of structural file data from .pdb file contents.

C++: core::io::pdb::create_sfr_from_pdb_file_contents(const std::string &) –> class core::io::StructFileRep

pyrosetta.rosetta.core.io.pdb.dump_multimodel_pdb(*args, **kwargs)

Overloaded function.

  1. dump_multimodel_pdb(poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, file_name: str) -> bool

Writes poses to a single PDB file, returns false if an error occurs

Use default StructFileRepOptions

C++: core::io::pdb::dump_multimodel_pdb(const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &, const std::string &) –> bool

  1. dump_multimodel_pdb(poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, file_name: str, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> bool

Writes poses to a single PDB file, returns false if an error occurs

C++: core::io::pdb::dump_multimodel_pdb(const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &, const std::string &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> bool

  1. dump_multimodel_pdb(poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, out: pyrosetta.rosetta.std.ostream) -> None

Writes poses to a given stream in PDB file format

Use default StructFileRepOptions

C++: core::io::pdb::dump_multimodel_pdb(const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &, std::ostream &) –> void

  1. dump_multimodel_pdb(poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, out: pyrosetta.rosetta.std.ostream, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

Writes poses to a given stream in PDB file format

C++: core::io::pdb::dump_multimodel_pdb(const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &, std::ostream &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

pyrosetta.rosetta.core.io.pdb.dump_pdb(*args, **kwargs)

Overloaded function.

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str) -> bool

Writes <pose> to a PDB file, returns false if an error occurs

Use default StructFileRepOptions

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, const std::string &) –> bool

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> bool

Writes <pose> to a PDB file, returns false if an error occurs

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, const std::string &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> bool

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream) -> None

  2. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, out_fname: str) -> None

Writes <pose> to a given stream in PDB file format

Use default StructFileRepOptions

If a non-empty string is given for the out_fname variable, then the Pose energy table at the bottom of the PDB will be labeled with this string.

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, std::ostream &, const std::string &) –> void

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

  2. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, options: pyrosetta.rosetta.core.io.StructFileRepOptions, out_fname: str) -> None

Writes <pose> to a given stream in PDB file format

If a non-empty string is given for the out_fname variable, then the Pose energy table at the bottom of the PDB will be labeled with this string.

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, std::ostream &, class std::shared_ptr<const class core::io::StructFileRepOptions>, const std::string &) –> void

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, mask: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) -> None

  2. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, mask: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

This version takes an AtomID mask.

Used by Will’s motif hash stuff, I think.

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, std::ostream &, const class core::id::AtomID_Map<bool> &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

  2. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, std::ostream &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: pyrosetta.rosetta.utility.io.ozstream) -> None

  2. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: pyrosetta.rosetta.utility.io.ozstream, filename: str) -> None

Writes a pose to a given stream in PDB file format, optionally

appending a given string and optionally extracting scores from the pose.

This came out of the 2016 Chemical XRW. It’s an attempt to preserve some stuff that jd2 was doing before, while centralizing all PDB generation in one place.

The pose to turn into a PDB.

Additional data to append to the PDB file data (from the job).

The output stream that the PDB file data will be written to.

(Optional) String for the filename. Will be included in the score data table if provided.

NOTE: The two booleans are now specified in the StructFileRepOptions. Job data is no longer used in JD3. Do not use this function for general pdb writing. Use dump_file.

Vikram K. Mulligan (vmullig.edu).

Jared Adolf-Bryfogle (jadolfbr.com)

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, const std::string &, class utility::io::ozstream &, const std::string &) –> void

  1. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: str) -> None

  2. dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: str, filename: str) -> None

Writes a pose to a given string in PDB file format, optionally

appending a given string and optionally extracting scores from the pose.

This came out of the 2016 Chemical XRW. It’s an attempt to preserve some stuff that jd2 was doing before, while centralizing all PDB generation in one place.

The pose to turn into a PDB.

Additional data to append to the PDB file data from the Job.

The output string that the PDB file data will be written to.

(Optional) String for the filename. Will be included in the score data table if provided.

NOTE: The two booleans are now specified in the StructFileRepOptions. Job data is no longer used in JD3. Do not use this function for general pdb writing. Use dump_file.

Vikram K. Mulligan (vmullig.edu).

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, const std::string &, std::string &, const std::string &) –> void

pyrosetta.rosetta.core.io.pdb.dump_pdb_residue(*args, **kwargs)

Overloaded function.

  1. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue) -> str

  2. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> str

  3. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, options: pyrosetta.rosetta.core.io.StructFileRepOptions, start_atom_number: int) -> str

PyRosetta-Compatible; Writes pdb data for the given residue, beginning from the given atom number

C++: core::io::pdb::dump_pdb_residue(const class core::conformation::Residue &, class std::shared_ptr<const class core::io::StructFileRepOptions>, unsigned long) –> std::string

  1. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, atom_number: int) -> str

  2. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, atom_number: int, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> str

PyRosetta-Compatible; Writes pdb data for the given residue, incrementing atom_number counter

C++: core::io::pdb::dump_pdb_residue(const class core::conformation::Residue &, unsigned long &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> std::string

  1. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, atom_number: int, out: pyrosetta.rosetta.std.ostream) -> None

  2. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, atom_number: int, out: pyrosetta.rosetta.std.ostream, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

Writes pdb data for the given residue, incrementing atom_number counter

C++: core::io::pdb::dump_pdb_residue(const class core::conformation::Residue &, unsigned long &, std::ostream &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

  1. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, out: pyrosetta.rosetta.std.ostream) -> None

  2. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, out: pyrosetta.rosetta.std.ostream, start_atom_number: int) -> None

  3. dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, out: pyrosetta.rosetta.std.ostream, start_atom_number: int, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

Writes pdb data for the given residue, beginning from the given atom number

C++: core::io::pdb::dump_pdb_residue(const class core::conformation::Residue &, std::ostream &, unsigned long, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

pyrosetta.rosetta.core.io.pdb.read_record_definitions_from_file(filename: str, record_type_map: pyrosetta.rosetta.std.map_std_string_core_io_pdb_RecordType) pyrosetta.rosetta.std.map_core_io_pdb_RecordType_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t

Return a mapping of PDB record types to record definitions.

C++: core::io::pdb::read_record_definitions_from_file(const std::string &, const class std::map<std::string, enum core::io::pdb::RecordType, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, enum core::io::pdb::RecordType> > > &) –> class std::map<enum core::io::pdb::RecordType, class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > >, struct std::less<enum core::io::pdb::RecordType>, class std::allocator<struct std::pair<const enum core::io::pdb::RecordType, class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > > > > >

pyrosetta.rosetta.core.io.pdb.store_base_residue_type_name_in_sfr(hetID: str, text_field: str, sfr: pyrosetta.rosetta.core.io.StructFileRep) None

Parse .pdb HETNAM text field to extract full resID and convert into SFR data.

C++: core::io::pdb::store_base_residue_type_name_in_sfr(const std::string &, const std::string &, class core::io::StructFileRep &) –> void